The identification through rare or private variants sequencing by WG, Exome or panels of selected genes, is widely used to develop new diagnostic and therapeutic approaches.
Here are some examples of such kind of projects in which the center is involved:
- Susceptibility of lung cancer in women with breast cancer (Young Researchers GR-2011-02350922)
- Identification of biomarkers in patients who have developed skin cancer after the kidney transplant (Targeted Research RF-2011-02347709)
- Characterisation of genes involved in diseases of motor neurons (Targeted Research RF-2011-02347127)
- Identifying causative variants of rare or unknown diseases
- Understanding the genetic basis of unresolved primary immunodeficiencies(PID), (Project Network NET-2011-02350069)
- Susceptibility to injury of the nasal septum after cocaine abuse in order to identify SNPs potentially responsible for an abnormal apoptotic response in epithelial tissues of these patients (Project financed by Pol Drug Dip)
- Study of the familial risk of prostate cancer (Project AIRC)
- Identification of new variants implicated in the pathogenesis of the Cornelia de Lange Syndrome (Parenti et al. 2015 Clinical genetics)
- Study of clonal populations of two consecutive relapses in a patient with myelodysplastic syndrome (MDS), through the analysis of somatic mutations identified by exome sequencing
Analysis of gene expression and the relationship between the expression of messenger RNA (mRNA) and RNA regulators, such as long non-coding RNA (lncRNA), small RNA etc.
It is fundamental for the understanding of the mechanism of gene regulation and pathways involved in various physiological and pathological phenotypes. The center is involved in studies of interaction between mRNA and smallRNA through transcriptomics data in animal models. Some examples:
- study of muscle development in myotonic dystrophy;
- study of the regulation of the development of axons;
- characterization of the transcriptional profile induced by miR-126 in mouse models of acute lymphoblastic leukemia, (iv) identification of microRNAs and genes involved in cell maturation invariant natural killer T cell (iNKT).
A similar approach has been used for studies of gene expression analysis in tuberculosis bacteria, under conditions of stress induced by exposure to different antibiotics and at different time points. The project involved the association of a given mRNA to smallRNA.
The analysis data of transcriptomics allowed, in other studies, the identification and the role of alternative splicing of genes and lncRNA involved in the response to oxidative stress in human endothelial cells, while it was used in breast cancer cells to detect the role of the KSRP protein in epithelial-mesenchymal transition mechanisms. In other project the center collaborated to determine the transcriptional profile of hematopoietic stem cells, treated with different viral vectors to test the efficiency of gene transfer.
The group also works on a study of transcriptomics used for the molecular characterization of the events of relapse of acute myeloid leukemia (AML).
Among the most recent research projects in which the Centre has been involved we report a study of post-transcriptional regulation in regulatory T cells (Young Researchers GR-2011-02346941), and a study for the characterization of the role of T cells and Follicular Helper their interaction with T Follicular Regulator in the development of pathogenic GC B cells in vivo, in mouse models of Type 1 diabetes and rheumatoid arthritis (Young Researchers GR-2011-02348732).
It is now known that in many diseases the environment plays a key role and that this role is manifested most often through an epigenetic modification. Some of the projects for which the center has given a key contribution are:
- Characterization of the profile of DNA methylation in cohorts of children and elderly people sensitized to various allergens (FP7 ATOPIC)
- Analysis of histone markers in mice subjected to the procedure model of syndromic forms of panic
- Analysis of the role of epigenetics in the development of panic disorder, in a parallel study of man and animal model, through characterization of the profile of DNA methylation in a cohort of monozygotic twins discordant for hypersensitivity to CO2, known endophenotype of panic disorder, and a mouse model of panic disorder and its intergenerational transmission
- Epigenetic basis of susceptibility to cardiovascular disease, possibly induced during fetal development
Due to the complexity of some research fields, it is sometimes necessary to have a more general and “enlarged” vision of the problem in order to answer the question being studied. For this reason it is sometimes necessary to integrate different types of analysis (genomics, transcriptomics, etc.). To follow some multi-omics studies, in which the center has been involved:
- Integrated study of genomics, transcriptomics, and epigenomics to identify genes and pathways involved in multiple sclerosis (Targeted Research RF-2011-02350347)
- Identification of the molecular mechanisms of Immuno-Evasion leukemia after allogeneic hematopoietic stem cell, through a multi-ohmic. (Targeted Research Project AIRC and RF-2011-02351998)
New bioinformatic tools
The center also focused on a number of projects to develop new tools for “omics” data analysis. In particular, it has been developed an algorithm for the analysis of quantitative data (expression, methylation) within pedigree families and an R package for the analysis of viral integration sites with a pipeline developed by TIGET.